KMS Of Academy of mathematics and systems sciences, CAS
| Quality control of single amino acid variations detected by tandem mass spectrometry | |
Yi, Xinpei1,3; Wang, Bo2; An, Zhiwu1,3; Gong, Fuzhou1,3 ; Li, Jing2; Fu, Yan1,3
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| 2018-09-15 | |
| Source Publication | JOURNAL OF PROTEOMICS
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| ISSN | 1874-3919 |
| Volume | 187Pages:144-151 |
| Abstract | Study of single amino acid variations (SAVs) of proteins, resulting from single nucleotide polymorphisms, is of great importance for understanding the relationships between genotype and phenotype. In mass spectrometry based shotgun proteomics, identification of peptides with SAVs often suffers from high error rates on the variant sites detected. These site errors are due to multiple reasons and can be confirmed by manual inspection or genomic sequencing. Here, we present a software tool, named SAVControl, for site-level quality control of variant peptide identifications. It mainly includes strict false discovery rate control of variant peptide identifications and variant site verification by unrestrictive mass shift relocalization. SAVControl was validated on three colorectal adenocarcinoma cell line datasets with genomic sequencing evidences and tested on a colorectal cancer dataset from The Cancer Genome Atlas. The results show that SAVControl can effectively remove false detections of SAVs. Significance: Protein sequence variations caused by single nucleotide polymorphisms (SNPs) are single amino acid variations (SAVs). The investigation of SAVs may provide a chance for understanding the relationships between genotype and phenotype. Mass spectrometry (MS) based proteomics provides a large-scale way to detect SAVs. However, using the current analysis strategy to detect SAVs may lead to high rate of false positives. The SAVControl we present here is a computational workflow and software tool for site-level quality control of SAVs detected by MS. It accesses the confidence of detected variant sites by relocating the mass shift responsible for an SAV to search for alternative interpretations. In addition, it uses a strict false discovery rate control method for variant peptide identifications. The advantages of SAVControl were demonstrated on three colorectal adenocarcinoma cell line datasets and a colorectal cancer dataset. We believe that SAVControl will be a powerful tool for computational proteomics and proteogenomics. |
| Keyword | Single amino acid variations Mass spectrometry Peptide identification False discovery rate Unrestrictive mass shift relocalization |
| DOI | 10.1016/j.jprot.2018.07.004 |
| Language | 英语 |
| Funding Project | Strategic Priority Research Program of CAS[XDB13040600] ; National Natural Science Foundation of China[31271416] ; National Key Basic Research Program of China[2015CB554406] ; Natural Science Foundation of Shanghai[17ZR1413900] ; International S&T Cooperation Program of China[2014DFB30010] ; NCMIS CAS |
| WOS Research Area | Biochemistry & Molecular Biology |
| WOS Subject | Biochemical Research Methods |
| WOS ID | WOS:000444789800013 |
| Publisher | ELSEVIER SCIENCE BV |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/31289 |
| Collection | 应用数学研究所 |
| Corresponding Author | Gong, Fuzhou; Li, Jing; Fu, Yan |
| Affiliation | 1.Chinese Acad Sci, Acad Math & Syst Sci, RCSDS, NCMIS, Beijing 100190, Peoples R China 2.Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Dept Bioinformat & Biostat, Shanghai 200240, Peoples R China 3.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China |
| Recommended Citation GB/T 7714 | Yi, Xinpei,Wang, Bo,An, Zhiwu,et al. Quality control of single amino acid variations detected by tandem mass spectrometry[J]. JOURNAL OF PROTEOMICS,2018,187:144-151. |
| APA | Yi, Xinpei,Wang, Bo,An, Zhiwu,Gong, Fuzhou,Li, Jing,&Fu, Yan.(2018).Quality control of single amino acid variations detected by tandem mass spectrometry.JOURNAL OF PROTEOMICS,187,144-151. |
| MLA | Yi, Xinpei,et al."Quality control of single amino acid variations detected by tandem mass spectrometry".JOURNAL OF PROTEOMICS 187(2018):144-151. |
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